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The microbiome composition of the hindgut is altered following weaning in dairy calves: impact of different weaning strategies
Composition of calf intestinal microbiota has immediate and long-term effects on health and productivity of the animal. Weaning stress may alter the colonization process due to dietary shifts and environmental factors. The objective of this study was to examine the effects of different weaning strategies on fecal microbiota of dairy calves. Twenty-four male and 20 female Holstein dairy calves were blocked according to gender and birth weight and randomly assigned into a step-down weaning (SW) or an abrupt weaning (AW) treatment at birth. Calves had free access to water and starter intake throughout the experiment and 9 L/d of milk until d 36 of life and weaned on d 49 of life. Calves in SW group were weaned gradually by reducing milk intake from 9 to 4.5 L/d from d 37 to d 48 while the AW calves were abruptly weaned on d 49 by reducing milk intake from 9 to 0 L/d. Fecal samples were collected on d 36 (pre-weaning) and on d 54 (post-weaning) of life. DNA was extracted and V4 region of 16S rRNA gene was amplified and subjected to paired-end Illumina sequencing. The output paired-end reads were merged using PANDASeq assembler and analyzed using QIIME. The resulted operational taxonomic units (OTUs) were aligned to Greengenes database. Alpha-diversity of bacterial community was calculated using different richness estimators. Differences in beta-diversity of microbiota across treatments and time points were tested using PERMANOVA. Diversity of fecal microbiota was low before weaning but increased significantly post-wean indicating new species benefited from dietary change. However, different weaning strategies did not affect alpha and beta-diversity measures. Before weaning, Firmicutes (49.2%) and Bacteroidetes (42.2%), Proteobacteria (3.8%), Tenericutes (1.7%), and Actinobacteria (1.5%) were predominant phyla. Another 16 phyla were present at low abundance; each less than 1% of population. After weaning, the percentage of Firmucutes and Actinobacteria decreased to 42% and 0.4%, while Proteobacteria, and Tenericutes increased to 5.6% and 3.9%, respectively. Different weaning strategies did not affect fecal bacterial population at the phylum level.
In total, 415 core OTUs, which is defined as OTUs shared amongst 50% or more of the calves, were different between pre- and post-wean. However, none of the core OTUs was affected by weaning strategies. Data showed fecal microbiota of dairy calves was undergoing a drastic change and became more diversified during the weaning process. However, weaning strategies had no substantial effect.
Keywords: Calves, fecal microbiota, weaning